ldt

L,D-transpeptidase involved in cell wall synthesis

locus: BSU_14040

pI: 10.25

mw: 17.59 kDa

protein length: 164 aa

gene length: 495 bp

function: cell wall biosynthesis

product: L,D-transpeptidase

essential: no

synonyms: ykuD

Genomic Context

categories

• [category|SW 1|Cellular processes] → [category|SW 1.1|Cell envelope and cell division] → [category|SW 1.1.1|Cell wall synthesis] → [category|SW 1.1.1.1|Biosynthesis of peptidoglycan]
• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.1|Biosynthesis of cell wall components] → [category|SW 2.6.1.1|Biosynthesis of peptidoglycan]
• [category|SW 4|Lifestyles] → [category|SW 4.2|Sporulation] → [category|SW 4.2.1|Sporulation proteins] → [category|SW 4.2.1.1|Spore coat proteins] → [category|SW 4.2.1.1.8|Not yet assigned]

Gene

Coordinates: 1,476,518 1,477,012

The protein

Protein family

• YkuD family (with [protein|456AF184261976FAA73359E81443F7035F457D07|YciB] and [protein|293794B65B9EEB7F049138F73893303BABFB9A2A|YqjB], according to UniProt)

Paralogous protein(s)

• [protein|293794B65B9EEB7F049138F73893303BABFB9A2A|YqjB]

[SW|Domains]

• contains a N-terminal N-acetylglucosamine-polymer-binding [SW|LysM domain] [Pubmed|18430080]
• [SW|LysM domain] (aa 2-45) (according to UniProt)

Structure

• [PDB|1Y7M] [Pubmed|16287140]
• [PDB|2MTZ] (complex with a peptidoglycan hexamuropeptide) [Pubmed|25429710]

[SW|Localization]

• spore wall (according to Swiss-Prot)

Expression and Regulation

Operons

• genes: [gene|6F256986E591DB82974A7F54EB1CE0C024A6F63B|ldt]
  description: [Pubmed|11011148]

  sigma factors

  • [protein|24F7FD5C7C3A68BB2760ABB8CBD8FBD65E5FF7D4|SigK]: sigma factor, [Pubmed|11011148], in [regulon|24F7FD5C7C3A68BB2760ABB8CBD8FBD65E5FF7D4|SigK regulon]

  regulatory mechanism

  • [protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA]: repression, [Pubmed|12850135], in [regulon|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA regulon]

  regulation

  • expressed during sporulation in the mother cell ([protein|search|SigK]) [Pubmed|11011148]

• genes: [gene|253A24EEA02C07E577A96FB64DF39F9A3D0C3A52|ykuE]-[gene|6F256986E591DB82974A7F54EB1CE0C024A6F63B|ldt]-[gene|DDAE68CD8D7F0D9C46E62D0EDBF4631C9EC4C236|ykuC]
  description: [Pubmed|22383849]

  regulation

  • expressed during sporulation in the mother cell ([protein|search|SigK]) [Pubmed|11011148]

Biological materials

Mutant

• MGNA-A766 (ykuD::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/766 NBRP B. subtilis, Japan]
• BKE14040 ([gene|6F256986E591DB82974A7F54EB1CE0C024A6F63B|ldt]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE14040 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAGTTTCCTCATCCTCCTTT, downstream forward: _UP4_TAATGTTTTCTTATTTGTTT
• BKK14040 ([gene|6F256986E591DB82974A7F54EB1CE0C024A6F63B|ldt]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK14040 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAGTTTCCTCATCCTCCTTT, downstream forward: _UP4_TAATGTTTTCTTATTTGTTT

References

Reviews

• 18430080

Original publications

• 12850135,11011148,17311917,22383849,22278298,22579252,16287140,25429710